Fluorescent labeling of transfer RNA and study of protein synthesis

ABSTRACT

Provided are methods for labeling transfer RNA comprising replacing the uracil component of a dihydrouridine of said transfer RNA with a fluorophore. The disclosed methods may comprise fluorescent labeling of natural tRNAs (i.e., tRNAs that have been synthesized in a cell, for example, in a bacterium, a yeast cell, or a vertebrate cell) at dihydrouridine (D) positions, or fluorescent labeling of synthetic tRNAs. In another aspect, the present invention provides methods for assessing protein synthesis in a translation system comprise providing a tRNA having a fluorophore substitution for the uracil component of a dihydrouridine in a D loop of the tRNA; introducing the labeled tRNA into the translation system; irradiating the translation system with electromagnetic radiation, thereby generating a fluorescence signal from the fluorophore; detecting the fluorescence signal; and, correlating the fluorescence signal to one or more characteristics of the protein synthesis in the translation system. The disclosed methods are useful in single molecule as well as in ensemble settings.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. Ser. No. 15/428,750, filedFeb. 9, 2017 (now allowed), which is a continuation of U.S. Ser. No.14/294,256, filed Jun. 3, 2014 (now U.S. Pat. No. 9,612,244), which is acontinuation of U.S. Ser. No. 12/664,952, filed Jan. 13, 2011 (now U.S.Pat. No. 8,785,119), which is the U.S. national stage entry ofPCT/US08/67735, filed Jun. 20, 2008, which claims the benefit ofpriority to U.S. Provisional Application Ser. No. 60/945,771, filed Jun.22, 2007, the entire contents of each of which are incorporated hereinby reference.

STATEMENT OF GOVERNMENT SUPPORT

This invention was made with government support under GM071014 andGM066267 awarded by the National Institutes of Health. The governmenthas certain rights in the invention.

FIELD

The invention relates to methods for labeling transfer RNA with afluorophore, and methods for the study of protein synthesis utilizing afluorophore-labeled transfer RNA.

BACKGROUND

Decoding of genetic information into protein sequences is a multi-stepprocess that requires specific charging of transfer RNA (tRNA) moleculeswith their cognate amino acids by their cognate aminoacyl-tRNAsynthetases (aaRSs) to faint aminoacyl-tRNA (aa-tRNA), specific bindingof aa-tRNAs to the ribosomal decoding center programmed with theircognate triplet codons, and large scale movements of tRNAs within theribosome as they shift progressively from the tRNA entry site (theA-site), to the peptidyl-tRNA site (the P-site), and finally to the tRNAexit site (the E-site), from which tRNA dissociation takes place.

While the elementary steps in elongation have been identified,additional studies will be required to achieve a full understanding ofthe molecular mechanisms of each step. Of particular interest is therole of tRNAs, which, rather than being passive and rigid substrates forthe ribosome, have been more recently implicated as being “active”players in the decoding process (Westhof, 2006), interacting stronglywith different sites on the ribosome and undergoing substantialconformational changes in migrating from the A- to P- to E-sites(Korostelev et al., 2006; Selmer et al., 2006). For example, a mutationin the D stem of tRNA^(Trp) (known as the Hirsh suppressor mutation(Hirsh, 1971) has been shown to promote miscoding at the anticodon.Recent kinetic studies show that this mutation specifically acceleratestwo forward steps on the ribosome: GTP hydrolysis for accommodation ofaa-tRNA to the A site and peptide bond formation (Cochella & Green,2005). Because this mutation is distal from the codon-anticodoninteraction, its ability to promote tRNA accommodation and peptide bondsynthesis suggests that the tRNA body is in direct communication withboth the decoding center of the 30S subunit and the GTPase center of the50S subunit. Another example is provided by the tertiary core ‘elbow’region of tRNA, which is formed by extensive interactions between the Dand T-loops. We have demonstrated, using single turnover rapid kineticsmeasurements (Pan et al., 2006; Pan et al., 2007), that mutations in theconserved G18:U55 base pair interfere with the ribosomal translocationstep, particularly for tRNA moving from the P- to the E-site, consistentwith X-ray crystallography results showing that position 55 is in directcontact with protein L1 in the E-site (Korostelev et al., 2006).

In existing studies, an important assay for the translocation rate isbased on fluorescent changes of modified natural tRNAs, isolated from E.coli or yeast cells, whose D residues have been replaced with proflavin(Wintermeyer & Zachau, 1979; Savelsbergh et al., 2003). However, thisapproach, as so far applied, suffers from two significant limitations.First, it does not allow direct monitoring of the movements of tRNAmutants on the ribosome. This is because mutant tRNAs, which areprepared by run-off in vitro transcription with T7 RNA polymerase(Sampson et al., 1989), lack D residues. As a result fluorescent A-sitetRNA has been used to monitor effects of mutation in P-site tRNA, andfluorescent P-site tRNA to measure effects of mutation in A-site tRNA.Second, proflavin is rapidly photobleached, rendering proflavin-labeledtRNA unsuitable for single molecule experiments in which fluorescentprobes are subject to high light fluxes. Interest in overcoming thislimitation is high, because recent work has clearly demonstrated thepotential of the single-molecule approach to yield more detailedmechanistic information about protein synthesis than is available fromensemble single turnover experiments (Blanchard et al., 2004a; Blanchardet al., 2004b).

The labeling of tRNA has been performed with respect to each of fourdifferent components of such molecules: (1) Amino acids. The amino groupof Lys-tRNA^(lys) was labeled with BODIPY FL by displacing itssuccinimidyl group (Woodhead, 2004), and the amino group ofMet-tRNA^(fMet) was acylated and reacted with maleimide to producefluorophore-Met-tRNA^(fMet), which, however, has reduced activitycompared to the unmodified molecule (McIntosh 2000). (2) 4-thioU(8)group. This has been used for the studies of aminoacyl-tRNA binding tothe ribosomal A site (Bieling et al, 2006; Blanchard, 2004a,b; Munro,2007). (3) acp³U47 group. It has only been labeled by the Blanchardgroup for their FRET studies (Blanchard, 2004a,b; Munro, 2007). (4)Dihydrouridine group. This group has been used to study the kinetics oftRNA binding and movements on the ribosome, but the choice of dye islimited to only proflavin, which, as described above, is very sensitiveto environment but is of little use for single molecule studies, whichrequire brighter dyes, or for FRET studies, which require a gooddonor-acceptor pair.

Since labeled tRNAs are so important for the studies of dynamics ofribosome function it is important to find a universal method of labelingmany tRNA species with many different dyes. All the above labelingmethods have their limitations. The amine reactive labeling of the aminoacid results in tRNAs that have low activities (McIntosh, 2000;Woodhead, 2004). The other three methods are dependent on the existenceof the modified group, so they can not be used if a transcribed tRNA,e.g., for the in vitro study of tRNA mutants, is required. For acp³U47,only 5 of the 20 amino acids have tRNAs that have a acp³ modificationfurther limiting its application on other tRNAs. 4-thioU and dihydroUare more prevalent modifications occurring in the 8th position, and Dloop, respectively (in E.coli only tRNA^(Glu), tRNA^(Lys), andtRNA^(Thr) do not have a 4-thioU modification, and only tRNA^(Glu) andtRNA^(Tyr) do not have a D modification). In ribosome studies, 4-thio Uhas been only successfully used with initiator tRNA, and our attempts tolabel an elongator tRNA proceeded with only modest yields. Furthermore,labeled Tyr-tRNA^(Tyr) showed very poor binding to ribosomes underconditions that are EF-Tu dependent.

Over the last decade, achievements have been realized through theapplication of new technologies to the life sciences, for example, wholegenome sequencing, DNA microarrays, and proteomic high-throughputanalysis. The data obtained with these technologies serve to underscoregaps remaining in the cellular information currently available. Two ofthese gaps are: 1) sensitive and efficient protein identification, and2) the dynamics of protein expression. Development of methods to detectprotein synthesis directly and in real time, identify the amino acidsequence of a protein, and localize such synthesis within a cell (liveproteomics) will enable fundamental advances in understanding basic lifeprocesses and aid significantly the search for new sources of therapy.See, for example, PCT Published Apps. WO 2004/050825 and WO 2006/228708.Protein synthesis monitoring (PSM) is an analytical method to identifyproteins being synthesized on single ribosomes, in live cells, and inreal time. In PSM, the protein synthesis apparatus is marked with aunique fluorescent labeling scheme, producing sequence-specific signalsthat enable protein identification. See, for example, PCT Published App.WO 2005/116252.

The study of cellular dynamics can utilize mRNA profiling in tissues andcells as a primary tool in research and clinical diagnosis. However,mRNA levels are uncertain predictors of protein expression. Currentproteomic analysis, based largely on 2D electrophoretic gels, massspectrometry, and combinatorial arrays, is limited by destructive samplepreparation, preventing both the real-time detection of proteins and theelucidation of the dynamics of cellular response to various modulators.A need exists in the art for reagents with increased sensitivity in asystem for studying cellular dynamics, such as Protein SynthesisMonitoring (PSM), which can measure protein synthesis by followingthousands of labeled ribosomes simultaneously and repeating themeasurements at any specific location for hours or days. Fluorescentlytranslation components with increased sensitivity in a protein synthesismonitoring system are needed to provide the ability to record thedynamic patterns of protein synthesis in live cells in vivo, or invitro.

SUMMARY

The present invention provides efficient methods for fluorescentlabeling of transfer RNA (tRNA). The methods for tRNA labeling enablethe assessment of protein synthesis in vitro or in vivo in one or moreliving cells with greater sensitivity that that which was possible inaccordance with prior methods, and overcome limitations related to rapidphotobleaching of traditional labeled tRNAs, such as proflavin-labeledtRNA. The present methods are useful in experiments to assess proteinsynthesis directly and in real time. For example, the methods enable therecording of the dynamic patterns of protein synthesis in live cells,including direct monitoring of the movements of tRNA or tRNA mutants onthe ribosome. The present methods are useful in single molecule as wellas in ensemble settings. Numerous other methods for assessing proteinsynthesis using the presently-disclosed fluorescently labeled tRNAs areprovided herein.

In one aspect, the present invention provides methods for labelingtransfer RNA comprising replacing the uracil component of adihydrouridine of said transfer RNA with a rhodamine fluorophore.

Also disclosed are nucleic acid compositions comprising a transfer RNAmolecule including a fluorophore substitution for the uracil componentof a dihydrouridine in a D loop of the transfer RNA. The fluorophorepreferably bears a primary amino group, and may be, for example, ahydrazide or a rhodamine fluorophore.

The present invention also provides methods for assessing proteinsynthesis in a translation system. In preferred aspects, such methodscomprise providing a tRNA having a fluorophore substitution for theuracil component of a dihydrouridine in a D loop of the tRNA;introducing the labeled tRNA into the translation system; irradiatingthe translation system with electromagnetic radiation, therebygenerating a fluorescence signal from the fluorophore; detecting thefluorescence signal; and, correlating the fluorescence signal to one ormore characteristics of said protein synthesis in said translationsystem.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 provides a scheme of an exemplary reaction for the labelling of aD-loop dihydrouradine residue.

FIG. 2 provides data pertaining to the optimization of the conditionsfor the labelling of tRNAs.

FIG. 3 provides the results of an experiment designed to comparefluorophore incorporation when a reduction step is omitted versus whensuch step is included.

FIG. 4 shows data derived from studies pertaining to the purification ofamino acid-charged, fluorophore-labeled tRNA.

FIG. 5 shows the results of time course studies of the rate of formationof the 30S initiation complex using labelled tRNA in accordance with thepresent invention.

FIG. 6 provides fluorescence spectra of “PRE”, “POST”, and “POST2”complexes.

FIG. 7 shows the kinetics of FRET change during translocation to formthe first POST complex on rapid mixing of EF-G.GTP with the PRE(DA),PRE(DU), or PRE(UA) complexes.

FIG. 8 provides data from a study of the activity of Cy3-tRNAPhe using apoly(Phe) assay.

DETAILED DESCRIPTION

The present invention may be understood more readily by reference to thefollowing detailed description taken in connection with the accompanyingfigures and examples, which form a part of this disclosure. It is to beunderstood that this invention is not limited to the specific products,methods, conditions or parameters described and/or shown herein, andthat the terminology used herein is for the purpose of describingparticular embodiments by way of example only and is not intended to belimiting of the claimed invention.

In the present disclosure the singular forms “a,” “an,” and “the”include the plural reference, and reference to a particular numericalvalue includes at least that particular value, unless the contextclearly indicates otherwise. Thus, for example, a reference to “atranslation component” is a reference to one or more of such componentsand equivalents thereof known to those skilled in the art, and so forth.When values are expressed as approximations, by use of the antecedent“about,” it will be understood that the particular value forms anotherembodiment. As used herein, “about X” (where X is a numerical value)refers to ±10% of the recited value, inclusive. For example, the phrase“about 8” refers to a value of 7.2 to 8.8, inclusive; as anotherexample, the phrase “about 8%” refers to a value of 7.2% to 8.8%,inclusive. Where present, all ranges are inclusive and combinable.

The disclosure of each patent, patent application, and publication citedor described in this document are hereby incorporated herein byreference, in their entirety. Full citations for each of thepublications cited herein may be found below in the paragraph followingthe heading “References Cited”.

In accordance with the present invention, provided are methods forlabeling transfer RNA comprising replacing the uracil component of adihydrouridine of said transfer RNA with a fluorophore. The disclosed,methods may comprise fluorescent labeling of natural tRNAs (i.e., tRNAsthat have been synthesized in a cell, for example, in a bacterium, ayeast cell, or a vertebrate cell) at dihydrouridine (D) positions. Forexample, the tRNA may have a dihydrouridine at one or more of positionsU16, U17, U20, and U20b. In some embodiments the transfer RNA may haveat least one uridine in its D loop, and in such embodiments the presentmethods may further comprise converting the uridine to dihydrouridineprior to replacing the uracil component with the fluorophore. Thus, thepresent methods may be used to label synthetic tRNAs (for example, tRNAtranscripts) and introducing D residues into these tRNAs with adihydrouridine synthase. Exemplary dihydrouridine synthases include,among others, Dus1p, Dus2p, Dus4p, and homologs or variants thereof. Inone embodiment, the dihydrouridine synthase Dus1p may be used to converta uridine at position U16 and/or position U17 of a tRNA. In anotherexample, the dihydrouridine synthase Dus2p may be used to convert auridine at position U20 of a tRNA. In yet another embodiment, thedihydrouridine synthase Dus4p may be used to convert a uridine atposition U20 and/or position U20b of a tRNA.

Using the unmodified transcript of E. coli tRNA^(Pro) as an example,which has U17 and U17a in the D loop, the present methods show thatDus1p catalyzes conversion of one of these uridines (mostly U17a) to D,and that the modified tRNA can be labeled with the fluorophoresproflavin and rhodamine 110, with overall labeling yields comparable tothose obtained with the native yeast tRNA^(Phe). This method permitsfluorescent labeling of, among other transcription components, in vitrosynthesized tRNA transcripts, which can contain mutations not found innature. Such labeled tRNAs have broad utility in research that involvesstudies of tRNA maturation, aminoacylation, and tRNA-ribosomeinteractions.

Labeling of a tRNA on one or more D positions may proceed in two steps(FIG. 1): first, reduction and opening of the heterocyclic uracil ringof dihydrouridine (for example, using sodium borohydride); then,replacing the base with a fluorophore bearing a primary amino group. Thedihydrouridine may be reductively cleaved to form a leaving group, whichmay be replaced by the fluorophore. The leaving group may be3-ureidopropanol.

The fluorophore with which the tRNA is labeled may be a rhodaminefluorophore. Suitable rhodamine fluorophores include rhodamine 110,rhodamine 123, rhodamine 6G, rhodamine B, and rhodamine 575, and thoseskilled in the art can readily identify additional rhodaminefluorophores for use in connection with the present methods. Therhodamine fluorophore may have a substituted secondary amine group.

Hydrazides are also good candidates for labeling of the tRNA. Moreover,reaction may proceed via a ribose present as an aldehyde, raising thepossibility of hydrazone formation (FIG. 1). There are rich supplies ofcommercially available dyes linked to a hydrazide group, such ascy3-hydrazide and cy5-hydrazides (FIGS. 1A and 1B), many of which aredesigned for FRET or single molecule studies. Exemplary hydrazidefluorophores include Cy3 hydrazide, Cy3.5 hydrazide, Cy5 hydrazide,Cy5.5 hydrazide, Alexa Fluor 488 hydrazide, Alexa Fluor 555 hydrazide,Alexa Fluor 568 hydrazide, Alexa Fluor 594 hydrazide, and Alexa Fluor647 hydrazide, Texas Red hydrazide, Lucifer yellow hydrazide,C5-DMB-ceramide, C₆-phosphatidylinositol 5-phosphate, Cascade Bluehydrazide, and ATTO dye.

The instant methods may further comprise “charging” or loading onto the3′ end of the tRNA an amino acid corresponding to a triplet nucleotidesequence that base-pairs to the anticodon sequence of the tRNA. Theloading of the amino acid onto the 3′ end of the amino acid may beperformed in vitro using known techniques (see, e.g., Examples 6 & 8,infra). Alternatively or additionally, the tRNA may be subjected toconditions that are effective to load the amino acid onto the 3′ end;for example, the tRNA may be introduced into the cellular environmentwhere the necessary covalent linkage is catalyzed by an aminoacyl tRNAsynthetase.

Also provided are nucleic acid compositions comprising a transfer RNAmolecule including a fluorophore substitution for the uracil componentof a dihydrouridine in a D loop of the transfer RNA. The fluorophorethat replaces the uracil component of the dihydrouridine may be inaccordance with the preceding description.

Introduction of rhodamine dyes into tRNA via substitution for uracilcomponents of dihydrouridine residues in the D-loop of tRNA has numerousadvantages. Nonlimiting advantages include: (1) Substitution proceedswith good retention of tRNA activity in protein synthesis; (2) A generalway of labeling tRNA molecules, most or all of which have dihydrouridineresidues in the D-loop is provided; (3) Rhodamines have rather lowquantum yields for photobleaching and are thus suitable for singlemolecule studies which utilize rather high light intensities.

Introduction of Rhodamine 110 into tRNAs containing dihydrouridineresidues may follow a preparation of tRNA^(Phe)(rhod16/17) in accordancewith the present invention. In addition, rhodamine-labeled tRNAs may beprepared having different fluorescence properties from those containingRhodamine 110, in order to be able to distinguish between differenttRNAs interacting with the ribosome during the course of a polypeptidesynthesis. For this purpose, rhodamines (RDs) may be utilized, which,like RD 110, contain primary or secondary amines symmetrically placed atthe 3- and 9-positions, allowing facile substitution for the dihydroUresidues. As demonstrated by Lee (1997), substitution on either thexanthylium or phenyl rings changes both the maxima and broadness offluorescence emission of rhodamines. A number of commercial rhodaminesare available that are potentially suitable for this purpose, includingRhodamines 110 and 123 from Invitrogen (Carlsbad, Calif.), and Rhodamine6G (Basic Red 1) from TCI America (Portland, Oreg.), which have emissionmaxima of 521 nm, 535 nm and 560 nm, respectively. Some exemplaryrhodamine structures are illustrated below. If further spectral variantsare needed, it will be possible to prepare other rhodamine derivatives,since their syntheses are straightforward using appropriatelysubstituted phthalic anhydrides and aminophenols, as shown in withrespect to the synthesis of rhodamine 575 (Scala-Valero, 1991).

Blanchard et al. (2004a,b) have employed different strategies forintroducing fluorescence into tRNA in single molecule FRET studies oftRNA:tRNA interaction on the ribosome, with the most generally usefulone for the present application being the alkylation of the 8-s⁴Unucleotide (e.g., with a Cy3 maleimide) that is found in many tRNAs.However, in preliminary experiments, it was found that alkylation oftRNA^(Phe) s⁴U with a fluorophore gave a derivative which wasconsiderably less active in polypeptide synthesis than eitherunderivatized tRNA^(Phe) or tRNA^(Phe) (rhod16/17), making its use forthis application disadvantageous. Nevertheless, given the ease of thealkylation reaction, the effects will be tested on polypeptide synthesisrates of alkylating other 8-s⁴U containing tRNAs, to see whetherderivatives prepared in this manner can be useful for the presentstudies.

In another aspect, the present invention provides methods for theassessment of protein synthesis in a translation system. Advantageously,such assessment may occur in real time, providing, inter alia, directinformation about the dynamics of protein expression, and can be used tostudy dynamic patterns of protein synthesis in vitro or in vivo. Thepresent methods for assessing protein synthesis in a translation systemcomprise providing a tRNA having a fluorophore substitution for theuracil component of a dihydrouridine in a D loop of the tRNA;introducing the labeled tRNA into the translation system; irradiatingthe translation system with electromagnetic radiation, therebygenerating a fluorescence signal from the fluorophore; detecting thefluorescence signal; and, correlating the fluorescence signal to one ormore characteristics of the protein synthesis in the translation system.The present methods are useful in single molecule as well as in ensemblesettings.

The fluorescently labeled tRNA may be prepared in accordance with themethods described herein. Labeled tRNAs may include an entire complementof tRNAs extant in a particular cell type, organism type, or organelletype (such as mitochondria or chloroplast), or may include a subset oftRNAs, such as some or all tRNAs that are cognate of a specific aminoacid, or a single type of isoaccepting tRNA that may be specific forone, two, or three different codons.

The translation system may comprise a cell-free (in vitro) system.Alternatively, the translation system may comprise a living cell. Theintroduction of a labeled tRNA into the translation system will accordwith the type of translation system in use; for example, if thetranslation system comprises a living cell, the introduction of thelabeled tRNA may comprise introducing the tRNA into the cellularenvironment. Those skilled in the art will readily appreciateappropriate techniques for introducing a tRNA into a living cell. Forexample, Sako et al. (2006) disclose a method for PTC suppressioncomprising introducing labeled suppressor tRNA into living cell therebyreading through PTC-containing mRNAS. Sako et al. show that introducingsuppressor tRNA to cells possessing a frameshift mutation, induced theupregulation of the corresponding mRNA and accumulation of the resultingprotein.

The present methods may further comprise providing at least oneadditional fluorescently labeled translation component. For example, theadditional fluorescently labeled translation component may be aribosome, a ribosomal protein, an initiation factor, an elongationfactor, a messenger RNA, or a ribosomal RNA. The fluorophore with whicha translation component is labeled may be a FRET partner (i.e., onemember of a FRET pair that comprises a FRET donor and a FRET acceptor)with the fluorophore with which the tRNA is labeled, such that thedetection of the fluorescence signal may comprise detecting energytransfer between the fluorophore of the translation component and thefluorophore of the tRNA.

Puglisi et al (U.S. Pat. No. 7,296,532) propose to use ribosomes, boundto a solid substrate through a specific attachment site, using labeledtRNAs as a FRET pair with another labeled component of the ribosomecomplex (usually a ribosomal protein), and using this labeled, cell-freetranslation system to monitor conformational dynamics and translationrates. For such techniques, the labeling methods for tRNAs disclosedherein are of particular use.

The irradiation of the translation system will also depend in part onthe type of translation system in use. For example, if the translationsystem comprises a cell-free system, the irradiation may compriseexposing all or part of the in vitro setting to the electromagneticradiation. If the translation system comprises a living cell (which maybe a population of living cells), the irradiation may comprise exposinga single cell, a desired subset of cells, or an entire population ofcells to the electromagnetic radiation. The electromagnetic radiationmay take any appropriate form. For example, the electromagneticradiation may comprise a wavelength of light that is sufficient toinduce fluorescence of the fluorophore with which the tRNA is labeled, afluorophore with which at least one additional component of thetranslation system is labeled, or both (i.e., the electromagneticradiation may comprise one or more different wavelengths, frequencies,intensities) In one example, where a FRET system is intended, theelectromagnetic radiation may be a laser light source that is sufficientto excite the fluorophore with which the tRNA is labeled such that itmay function as a donor fluorophore and thereby emit energy sufficientto excite one or more accepting fluorophore that is bound to one or morerespective components of the translation system. Depending on the typeof fluorophore with which the tRNA is labeled, and, where applicable,the type of fluorophore with which at least one additional component ofthe translation system is labeled, as well as other factors such as theopacity of the translation system, the electromagnetic radiation maycomprise one or more specific wavelengths, frequencies, or intensities,and may be applied for an appropriate duration, in accordance withvarious factors that those skilled in the art will readily appreciate.

The irradiation of the translation system directly or indirectly resultsin the generation of a fluorescence signal from the fluorophore withwhich the tRNA is labeled. In accordance with the present invention, thefluorescence signal is detected using an appropriate means. Detectionmeans may include the use of one or more of photodiodes,phototransistors, photomultipliers, charge-coupled device cameras, orany other appropriate device or arrangement of devices. The signal maycorrespond to simple fluorescence, FRET, lifetime, or anisotropy, andrelate to the frequency, sequence, intensity, or any other relevantparameter of the detected fluorescence and/or its relationship to otherevents occurring in the translation system—whether protein synthesisactivity other aspect of the state of a translation system—as will bediscussed more fully herein.

The conversion of the detected signal to data and the interpretation ofthe data may be performed using any appropriate devices and techniques;those skilled in the art will be familiar with numerous suitable devicesand techniques. The fluorescence signal may therefore be correlated toone or more characteristics of the protein synthesis that occurs withinthe translation system. Characterization of real time protein synthesisrepresents a fundamental advance in the efforts to understand bothnormal and abnormal cellular processes. Protein synthesis monitoring(PSM), a technique with which those skilled in the art will be familiar,utilizes a fluorescent labeling scheme for tRNAs and ribosomes toproduce optical signals for identifying the synthesized proteins. PSMmay be used to monitor thousands of labeled ribosomes simultaneously,recording, analyzing and comparing patterns of protein synthesis in avariety of live cells and tissues, which can be repeated over hours anddays. See, e.g., PCT Application WO 2005/116252. In one example, acell-free, prokaryotic polypeptide translation system is labeled, thesignals produced captured and analyzed, and the polypeptides beingsynthesized is identified. The methods for in vitro protein synthesisadvance the technology to full-length proteins, and to observations inlive cells. The methods for labeling tRNA utilized in PSM may result inapplications in drug discovery and diagnostics. Other exemplarycharacterization parameters and general techniques may be found in U.S.Pat. No. 7,296,532 to Puglisi, et al., and the present methods forassessing protein synthesis are fully applicable and adaptable to theuses described in that patent.

Fluorescence resonance energy transfer (FRET) occurs between twoneighboring fluorophores when the emission spectrum of one (the donor)overlaps the excitation spectrum of the second (the acceptor). FRET ismediated by dipole-dipole interactions, where the excitation energyabsorbed by the donor is transferred to the acceptor. The result of thisexchange of energy is seen as a decrease in the specific emissionintensity of the donor and an increase in the specific emissionintensity of the acceptor.

The drive for increased throughput within the drug discovery process hasprompted a new phase of assay development combining miniaturisation withautomation. In parallel, there has also been a concerted effort to shiftfrom conventional radiometric detection technologies to those basedaround fluorescence. The technique of FRET provides a non-radiometricroute for the detection of numerous biological interactions inhomogenous assay formats. FRET describes the transfer of excitationenergy from a donor fluorophore to an acceptor chromophore when the twodye molecules are separated by <100 Å and overlap occurs between thedonor emission, and acceptor absorption spectra. Pursuant to the presentinvention, protein-DNA and protein-peptide binding events have beenexamined using FRET combined with fluorescent imaging.

In one exemplary embodiment of the present methods of assessing proteinsynthesis, the at least one additional fluorescently labeled translationcomponent may comprise a ribosome, wherein the introduction of saidlabeled tRNA into the translation system contacts the labeled tRNA withthe fluorescently labeled ribosome, and the method further comprisesdetecting a timed sequence of Fluorescence Resonance Energy Transfer(FRET) signals characteristic of one or more polypeptides synthesized bythe ribosome in order to identify at least one of the polypeptides. Inanother aspect, the present methods may involve the direct monitoring ofthe movements of tRNA or tRNA mutants on the ribosome. One exemplarymethod for measuring protein synthesis in vitro or in vivo from one ormore living cells involves the production of a transient FRET signalwhen a specific tRNA is processed by the ribosome. For example, thetechnique may involve a) the preparation of E. coli ribosomesincorporating a fluorescent label in protein L11, which is proximal tothe entry (A-site) of tRNA binding to the ribosome and/or in protein L1,which is proximal to the tRNA exit (E-site) of the ribosome, and b) thepreparation of fully functional fluorophore-substituted tRNAs, e.g., arhodamine labeled tRNA, which are capable of acting as FRET donors oracceptors when bound in the A or E-sites of appropriatefluorescent-labeled ribosomes.

Proflavin-substituted tRNA^(Phe), tRNA^(Phe) (prf 16/17), prepared viareduction of dihydroUs at positions 16 and 17 with NaBH₄ and replacementof the resulting ureidopropanol with proflavin (Wintermeyer, 1979), hasbeen used in stopped-flow studies of tRNA interaction with the ribosome(Pape, 1998). As proflavin is not a suitable chromophore for singlemolecule studies, proflavin was substituted by rhodamine 110, which hasacceptable brightness and stability for single molecule studies.tRNA^(Phe) (rhod16/17) derivative is fully functional, both as anacceptor of Phe in the PheRS-catalyzed charging reaction and inpoly(U)dependent poly(Phe) synthesis. This tRNA derivative has afluorescence maximum at 530 nm on excitation at 497 nm, making it asuitable donor in FRET studies with Cy3 as acceptor (Forster R₀ of ˜67Å). In ongoing stopped-flow work, a FRET signal was detected when theternary complex EF-Tu.GTP-PhetRNA^(Phe) (rhod16/17) binds to ribosomeslabeled with Cy3-L11 which are programmed with mRNA022 and containfMet-tRNA^(fmet) in the P-site and an empty UUU-programmed A-site. TheFRET signal has maximal intensity on initial binding of the ternarycomplex to the A/T site of the ribosome and GTP hydrolysis, anddecreases in intensity as inorganic phosphate (P_(i)) and EF-Tu.GDP arereleased and Phe-tRNA^(Phe) is accommodated into the A-site. The t_(1/2)for this decrease is ˜250 ms. When the reaction is performed in thepresence of kirromycin (Kir), an antibiotic which allows ternary complexbinding and GTP hydrolysis but inhibits P_(i) and EF-Tu.GDP release, theinitial higher FRET state is maintained. This result demonstrates that aclear FRET signal is observed on entry of a charged tRNA into theribosomal A-site.

EXEMPLARY EMBODIMENTS Example 1—Specific Introduction of a D ResidueInto an E. coli tRNAPro/UGG Transcript by Yeast Dus1p

The present methods use the yeast enzyme Dus1p (Xing et al., 2004),expressed in E. coli as a His-tag fusion, to introduce a D residue intoan in vitro tRNA transcript. Dus1p catalyzes U→D conversion specificallyat positions 16 and 17 of tRNAs, utilizing FAD as a cofactor and NADHand NADPH as electron donors (Xing et al., 2004). Because virtually alltRNA genes in databases encode U16, U17, or both, this approach allowsintroduction of D residues at these positions, thus creating potentialsites for fluorescent labeling. The heterocyclic ring of D is subject toreductive cleavage by sodium borohydride, yielding 3-ureidopropanolbound to the ribose C-1′ position (Cerutti & Miller, 1967), which is afacile leaving group that is readily replaced by fluorophores bearing aprimary amino group (Wintermeyer & Zachau, 1974). Second, it is hereindemonstrated that rhodamine 110, a photobleaching-resistant fluorophorecommonly used in single-molecule studies, which also has a strongeremission intensity than the dyes used by Wintermeyer and Zachau (1974),is competent for such replacement, generating a fluorescent-labeled tRNAthat is active in protein synthesis

The transcript of E. coli tRNA^(Pro/UGG), prepared by in vitro run-offtranscription and containing U residues at positions 17, 17a, and 20,was subjected to modification by Dus1p. The amount of U→D conversion wasdetermined by a previously established colorimetric method (Jacobson &Hedgcoth, 1970) which measures the amount of acyclic ureido group formedby alkaline cleavage of the D ring. Calibration of the assay withdihydrouracil reveals a linear relationship between absorption andconcentration of ureido group. Application of this assay to bulk tRNAisolated from E. coli yields an average number of D per E. coli tRNA of1.5±0.5 (Table 1), similar to the previously determined value of 1.4±0.1(Jacobson & Hedgcoth, 1970). The number of D residues per transcript ofE. coli tRNA^(Pro/UGG) modified with Dus1p (2.7 μM), determined over arange of transcript concentrations (16-40 μM), was 0.97±0.01 (Table 1,below), indicating that only one of the three U residues at 17, 17a, and20 was converted to D.

TABLE 1 Number of D residues per tRNA tRNA D Content D/tRNA (μM) OD₅₅₀(μM) D/tRNA Average E. coli 0 0 0 0 0.97 ± 0.2 tRNA^(Pro/UGG) 16 0.1015.3 0.96 24 0.19 27.5 1.15 32 0.20 30.0 0.94 40 0.23 33.5 0.84 E. coli0 0 0 0 1.5 ± 0.5 total tRNA 8 0.12 17.5 2.2 16 0.17 25 1.6 32 0.27 391.2 40 0.32 47 1.2

To map the site of modification within the transcript, D was convertedto a ureido group, which blocks primer extension (Xing et al., 2004). Anoligonucleotide primer was designed to complement G42 to G22 in E. colitRNA^(Pro/UGG) and the products of primer extension were analyzed bydenaturing polyacrylamide gel electrophoresis (PAGE). This analysisidentifies position G18 in the Dus1p-modified transcript as a major stopsite, not seen with the unmodified transcript, indicating that the U→Dmodification catalyzed by Dus1p occurs at U17a, rather than at U17.Although the mechanism of how Dus1p recognizes tRNA is unknown at thepresent, the demonstrated specificity at U17a, which is immediatelyadjacent to the conserved G18-G19 sequence common to all tRNA species,suggests that this enzyme may recognize G18-G19 as the determinant formodification. The product of Dus1p modification is denoted as E. colitRNA^(Pro/UGG)(D-17a).

Example 2—Rhodamine Labeling of D-Containing tRNAs

In vitro transcribed E. coli tRNA^(Pro/UGG)(D-17a) was labeled witheither proflavin or rhodamine 110, using standard reductive cleavageconditions (leading to incorporation values of 1.0 and ˜0.5,respectively, and giving rise to labeled tRNAs denoted tRNA^(Pro)(prf)and tRNA^(Pro)(rhd), respectively. Labeling stoichiometries weredetermined from the ratio of absorption in the visible (462 nm forproflavin, 512 nm for rhodamine 110) to that at 260 nm for tRNA(corrected for a contribution from the dye). The lower stoichiometry inthe case of rhodamine may be due to its expected lower nucleophilicityas compared with proflavin, given its much lower pKa value [rhodamine110, 4.3 (Boonacker & Van Noorden, 2001); proflavin, 9.6 (Horobin etal., 2006)] and its somewhat more hindered primary amine. Similarly,labeling of native yeast tRNA^(Phe), which contains D residues atpositions 16 and 17, under the same conditions led to incorporationvalues of 2.0 and 1.0 for proflavin or rhodamine 110, respectively, andgiving rise to labeled tRNAs denoted tRNA^(Phe)(prf) andtRNA^(Phe)(rhd), respectively.

Example 3—Biochemical Characterization of Fluorescent-Labeled tRNAs

tRNA^(Pro)(prf), tRNA^(Phe)(prf) and tRNA^(Phe)(rhd) are each goodsubstrates for their respective synthetases, with ˜75% efficiency ofaminoacylation of tRNA^(Pro)(prf) as compared with the unlabeledtranscript (900 pmol/A₂₆₀ versus 1200 pmol/A260), and 85% and 77% ofaminoacylation of tRNA^(Phe)(prf) (1100 pmol/A₂₆₀) and tRNA^(Phe)(rhd)(1000 pmol/A₂₆₀), respectively, as compared to the unlabeled tRNA^(Phe)(1300 pmol/A₂₆₀). The results with tRNA^(Phe)(prf) parallel thosereported earlier (Wintermeyer & Zachau, 1979).

In contrast, aminoacylation of purified tRNA^(Pro)(rhd) gave quite lowPro incorporation, ˜10% as compared with the unlabeled transcript. Herethe labeled transcript was purified away from unlabeled transcript by arecently developed method (Hou et al., 2006) in which oligonucleotidecomplementary to the site of the label is hybridized to the unmodifiedtranscript. Since labeled transcript is inaccessible to suchhybridization, subsequent RNase H digestion allows selective removal ofunmodified transcript. The ˜10% level of aminoacylation activitysuggests that ProRS is inhibited by the presence of the bulkierrhodamine group in the tRNA tertiary core to a much greater extent thanwhen the tRNA is proflavin-labeled. These results are consistent with aprevious finding that this enzyme is sensitive to structural alterationsin the core (Liu & Musier-Forsyth, 1994) and support the notion that thestructure of the tRNA tertiary core is a determinant for aminoacylationby ProRS. Thus, while PheRS can easily accommodate rhodamine in the tRNAtertiary core, ProRS cannot. The contrast between these two enzymesillustrates the idiosyncratic nature of aminoacyl-tRNA synthetases withrespect to their sensitivity to the structure of the tRNA tertiary core.

Phe-tRNA^(Phe)(rhd) was also tested for its ability to participate inribosome-catalyzed poly(U)-dependent poly(Phe) synthesis, giving ratesand extents of reaction similar to those obtained with unlabeledPhe-tRNA^(Phe).

Example 4—Fluorescent Labeling of tRNA Utilizing Dus Enzymes toIntroduce D Residues into a tRNA Transcript

A general method is provided for fluorescent labeling of tRNA thatutilizes one of the Dus enzymes to introduce D residues into a tRNAtranscript and subsequently replaces the D residues with a primaryamine-containing fluorophore such as proflavin or rhodamine 110. Themethod is general for tRNA species, because all but a small number oftRNAs have U residues in the D loop that are substrates for the Dusenzymes (Sprinzl et al., 1998). Even in the rare cases where U is absentfrom a tRNA (e.g. Steptomyces lividans tRNA^(Cys)), it may be possibleto introduce a U into the D loop by site-directed mutagenesis, either asa replacement or as an insertion, as long as the introduced U does notalter the normal functions of the tRNA. Here the focus was on yeastDus1p, which is specific for U16 and U17. Other yeast enzymes arespecific for U20 (Dus2p) and for U20 and U20b (Dus4p) (Xing et al.,2004). Although not as fully characterized, E. coli also encodes severalDus enzymes (Bishop et al., 2002), which offer additional options forintroducing D residues. Thus, the potential to use the described methodfor fluorescent labeling of tRNA is virtually unlimited.

The present labeling methods should prove useful in a wide variety ofresearch involving tRNAs. One immediate application is to use themethods to directly monitor the dynamic interaction of mutant tRNAs withthe ribosome (Pan et al., 2006; Pan et al., 2007), but other tRNA-enzymereactions are amenable to this approach as well. Since tRNA^(Pro)(prf),tRNA^(Phe)(prf) and tRNA^(Phe)(rhd) are good substrates for theirrespective synthetases, such labeled tRNAs can be used to yield insightsinto tRNA conformational rearrangements upon interaction with itscognate tRNA synthetase. Also, because eukaryotic tRNAs are believed tobe channeled through a multi-synthetase complex (Negrutskii & Deutscher,1991), the technique may be used to study the dynamics of themulti-synthetase complex assembly. Other possibilities include enzymaticreactions that occur during maturation of tRNA, such as 5′ processing,intron splicing, anticodon modification, and CCA end addition. Finally,the described method will be also useful for studying the kinetics andthermodynamics of tRNA folding, which provides the basis forunderstanding the folding of larger RNA molecules such as ribozymes.

Example 5—Replacement of D Residues with Cy-hydrazides

Yeast tRNA^(Phe) has D residues at positions 16 and 17. Labeling ofyeast tRNA^(Phe) with Cy3 hydrazide was initially attempted by using thetwo-step procedure previously employed to label the D positions withproflavin or rhodamine 110 (Wintermeyer and Zachau, 1979; Betteridge,2007), in which reduction of the D residue by treatment with NaBH₄ atneutral pH and room temperature is followed by reaction with 2 mM dye atpH 3, 37° C. for 45′ to 90′. However, utilization of these conditionsled to very poor incorporation of dye (<0.05 Cy3/tRNA as compared withessentially stoichiometric incorporation of proflavin (1.7-2.0 prf/tRNA(Pan, 2007)) and considerably higher incorporation of rhodamine 110(1.0/tRNA (Betteridge, 2007)).

A systematic study of dye uptake as a function of pH and time ofincubation (FIG. 2) was undertaken. In each reaction in (FIG. 2A-C) 200pmol of NaBH₄-treated tRNA^(Phe) was mixed with Cy3 in 100 μl of 0.1 Meither Na formate (pH<4), Na acetate (pH 4 and 5), or Na phosphatebuffer (pH≥6). After the reaction pH was brought up to 7.5 to stop thereaction, and phenol extractions and ethanol precipitations wereperformed to remove excess dyes before OD measurements. FIG. 2A relatesto dye concentration dependence: pH=3.0, incubation time 1 hr,temperature 37° C. FIG. 2B relates to pH dependence: [Cy3]=4 mM,temperature 37° C., incubation time 2 hr. FIG. 2C relates to timedependence. [Cy3]=4 mM, temperature 37° C., pH 3.7.

These studies led to the choice of pH 3.7 and 2 hrs as preferred. Underthese conditions, dye incorporation increased linearly with dyeconcentration in the range 0.5 mM-4 mM, reaching 0.15 Cy3/tRNA at 4 mM.Further increasing Cy3 hydrazide concentration to 40 mM yielded anuptake of 1.2-1.3 Cy3/tRNA^(Phe). Application of the high concentrationprocedure to other tRNAs and to substituting Cy5 hydrazide for Cy3hydrazide afforded the following results: 0.94 Cy3/E. coli tRNA^(arg) (2D residues); 0.39 Cy5/E. coli tRNA^(fMet) (1 D residue).

In addition to D residues, yeast tRNA^(Phe) has a wybutine base atposition 37. This base can be excised and replaced with primary aminenucleophiles attached to dyes by prolonged incubation at pH 2.9 withoutthe need for NaBH₄ reduction, although the overall reaction was found toproceed more slowly than substitution at the D positions following NaBH₄reduction (Thiebe and Zachau, 1968; Wintermeyer and Zachau, 1971;Wintermeyer and Zachau, 1979).

To test whether substitution at position 37 was competitive withsubstitution at the D positions under the optimized conditions describedabove, a direct comparison of dye incorporation was made between whenthe NaBH₄ step is omitted versus when it is included (FIG. 3). 400 pmolof NaBH₄-treated or untreated tRNA^(Phe) was labeled with Cy3 using thestandard protocol (see Example 8, infra, Materials and Methods). Peaksat 260 and 550 nm corresponds to absorption of tRNA and Cy3,respectively.

Consistent with the earlier work, values of dye incorporation of ≤0.08and 1.2 Cy3/tRNA, respectively, were obtained, demonstrating thatvirtually all of the dye is incorporated into the D positions.

Example 6—Optimization of the Charging of Cy3-Labeled Phe-tRNA^(Phe)

Synthesis of charged, Cy3-labeled tRNA^(Phe) for use in functionalstudies may be considered to be a three-step procedure, involving NaBH₄reduction, labeling with Cy3 hydrazide, and charging by Phe-RS. Sincereduction must precede labeling, there are three options for how thesesteps are sequenced: 1) charging-reduction-labeling; 2)reduction-labeling-charging; or 3) reduction-charging-labeling.Option 1) was found to yield poor results, because of the high labilityof Phe-tRNA^(Phe) toward NaBH₄ treatment, which in our hands results ina 90% loss of Phe from the tRNA. Option 2) was also found to benon-optimal, because Cy3-labeled tRNA^(Phe) is less efficiently chargedby Phe-RS under standard conditions than unlabeled tRNA^(Phe). Forexample, tRNA^(Phe) containing 1.3 Cy3s charges to a level of 480 pmolPhe/A₂₆₀, approximately 2-fold lower than the level of ˜900 pmolPhe/A₂₆₀ obtained with unlabeled tRNA^(Phe).

The best results were obtained with option 3. FIG. 4A depicts theresults of purification of Phe-tRNAPhe that was charged after NaBH₄treatment using a reverse-phase column on HPLC. FIG. 4B depicts theresults of purification of Cy3-Phe-tRNA^(Phe) using a Mono-Q column onFPLC. In the preferred procedure, shown in FIG. 4A, the reduction andcharging steps were followed by RP-HPLC to separate charged fromuncharged material (FIG. 4A), and the charged fraction was labeled with40 mM Cy3 hydrazide at pH 3.7 as described above. The final material wassubjected to FPLC (FIG. 4B), leading to a major fraction, denotedPhe-tRNA^(Phe)(Cy3), containing 1.0 Cy3/tRNA^(Phe) and charged to alevel of 1190 pmol Phe/A₂₆₀. Here the choice of pH 6.0 for the elutingbuffer is preferred, since higher pH leads to loss of Phe, whereas lowerpH leads to loss of Cy3. Similar FPLC of the Cy5-labeledfMet-tRNA^(fMet) prepared as described above via option 2) and with noRP-HPLC purification resulted in partially purified material denotedfMet-tRNA^(fMet)(Cy5), containing 0.75 Cy5/tRNA^(fMet) and charged to alevel of 590 pmol fMet/A₂₆₀. FIG. 4C illustrates the retention of[³H]-Phe and Cy3 with tRNA^(Phe) following incubation of[³H]-Phe-tRNA^(Phe)(Cy3) at 37° C. for 2 hr at various pH values.[³H]-Phe was determined by TCA precipitation and counting. Cy3 wasdetermined following ethanol precipitation. Buffers were the same as thestudy shown in FIG. 2B.

The observation that pH 3.7, which is preferred for reduced tRNA^(Phe)labeling by Cy3 (FIG. 2B), would lead to unacceptable loses of Cy3 onisolation of Cy3-labeled tRNA^(Phe) is readily explainable. Raising theconcentration of hydrazide shifts the equilibrium shown in FIG. 1 in thedirection of imine formation, consistent with our results, and theweakly acidic pH optimum for the rate of hydrazide adduct formation isin accord with results published for similar condensations (Jencks,1964). On the other hand, isolation of Cy3-labeled tRNA is carried outunder conditions in which hydrolysis of the hydrazide adduct isessentially irreversible, mandating the use of a higher pH tokinetically trap the adduct, the hydrolysis of which is alsoacid-catalyzed.

Example 7—Functional Assays

Formation of 30S initiation complex (30SIC). Previous studies have shownthat the rate of 30SIC formation can be monitored by changes influorescence, using either a proflavin derivative of fMet-tRNA^(fMet)[fMet-tRNA^(fMet)(prf)] (Grigoriadou, 2007a) or a coumarin (Grigoriadou,2007a) or Cy3 (Qin, 2008) derivative of IF2. Here, stopped-flowfluorescence measurements using limiting amounts of either IF2^(Cy3)(prepared as described: Qin et al., in preparation) orfMet-tRNA^(fMet)(Cy5), were carried out with 0.3 μM 30S subunits at 20°C., essentially as described (Grigoriadou et al., 2007b). UsingfMet-tRNA^(fMet)(Cy5) a rate of 30SIC formation that was essentially thesame as that measured from Cy3-IF2 (FIG. 5) was obtained, suggestingthat Cy5-fMet-tRNA^(fMet) is fully functional in formation of 30SIC.FIG. 5A shows the fluorescence change of Cy3-IF2. The trace was fit to asingle exponential term with a rate of 21±2 s⁻¹, and a slope term. FIG.5B shows the fluorescence change of Cy5-fMet-tRNA^(fMet). The trace wasfit to a single exponential term with a rate of 19±1 s⁻¹, and a slopeterm. Excitation was at 530 nm or 650 nm and fluorescence was monitoredthrough a bandpass filter (550±10 nm or 680±10 nm) for IF2^(Cy3) orfMet-tRNA^(fMet)(Cy5), respectively.

Formation and Translocation of a Pre-Translocation (PRE) Complex.

Three samples of PRE complex made with mRNA-MFK programmed ribosomeswere formed in parallel, by addition of: i) both fMet-tRNA^(fMet)(Cy5)and Phe-tRNA^(Phe)(Cy3) (the donor-acceptor or DA sample); ii) unlabeledfMet-tRNA^(fMet) and Phe-tRNA^(Phe)(Cy3) (the donor alone or DU sample);and iii) fMet-tRNA^(fMet)(Cy5) and unlabeled Phe-tRNA^(Phe) (theacceptor alone or UA sample). These complexes resulted in fMetPheformation, and were purified by ultracentrifugation through a sucrosecushion prior to their utilization in the fluorescence measurementsdescribed below. The stoichiometries of fMetPhe formed, and of [³H]-Pheand [³³S]-fMet cosedimenting with the ribosome (see Table 2, below), arevery similar whether using Cy3-labeled or unlabeled Phe-tRNA^(Phe) (DUand DA samples vs. UA sample) or Cy5-labeled or unlabeledfMet-tRNA^(fMet) (UA and DA samples vs. DU sample), providing aconvincing demonstration of the functionality of the Cy-labeled tRNAs inbinding to the ribosome and participating in dipeptide formation, aspart of PRE complex formation.

TABLE 2 Stoichiometry of complexes formed with labeled tRNAs Rel.fMetPhe/ donor fMet/70S Phe/70S Lys/70S 70S Cy5/70S Cy3/70S decrease PRE0.71 ± 0.03 0.78 ± 0.06 0 0.55 ± 0.03 0 0.75 ± 0.02 ND (DU) PRE 0.64 ±0.05 0.63 ± 0.05 0 0.48 ± 0.04 0.63 ± 0.02 0 ND (UA) PRE 0.74 ± 0.030.68 ± 0.04 0 0.54 ± 0.03 0.61 ± 0.04 0.71 ± 0.03 0.54 (DA) POST 0.62 ±0.03 0.64 ± 0.04 0 ND 0.21 ± 0.02 0.70 ± 0.03 0.32 (DA) POST2 0.63 ±0.03 0.58 ± 0.04 0.57 ± 0.05 ND 0.13 ± 0.02 0.05 ± 0.02 0 (DA)

FIG. 6 shows the fluorescence spectra of PRE (FIG. 6A), POST (FIG. 6B),and POST2 (FIG. 6C) complexes. DA, Cy3-tRNAPhe+Cy5 tRNAfMet; DU,Cy3-tRNAPhe+unlabeled tRNAfMet; UA, unlabeled tRNAPhe+Cy5 tRNAfMet.Fluorescence spectra of the three PRE samples (FIG. 6) provide clearevidence of FRET in the DA sample, as shown by the increase in acceptorand decrease in donor fluorescent intensities relative to the A and Dsamples, respectively. Addition of EF-G.GTP to each of the samplesleading to post-translocation (POST) complex formation results in amarked decrease in FRET efficiency, as evidenced by the decreasesobserved between the DA sample and both the UA and DU samples (FIG. 6;Table 2). This decrease in FRET efficiency is consistent with anincrease of 14 Å in the distance between the dihydrouracil positions oftRNA^(Phe) and tRNA^(fMet), calculated from coordinates determined byX-ray crystallographic analysis of ribosome-bound tRNAs (Yusupov et al.2001), as these two tRNAs move from occupying the A- and P-positions,respectively, in the PRE complex (28 Å apart), to occupying the P- andE-positions, respectively, in the POST complex (42 {acute over (Å)}apart). Addition to the three PRE samples of both EF-G.GTP and the nextcognate ternary complex, EF-Tu.GTP.Lys-tRNA^(Lys) ternary complexreduces FRET efficiency to zero (FIG. 6C), consistent with the expectedremoval of tRNA^(fMet) from the ribosome on A site binding andtranslocation of Lys-tRNA^(Lys) to form the POST2 complex. FIG. 6D is aschematic showing transition from PRE to POST to POST2.

The kinetics of FRET change during translocation to form the first POSTcomplex on rapid mixing of EF-G.GTP with the PRE(DA), PRE(DU), orPRE(UA) complexes are displayed in FIG. 7, in which “Acceptor”=monitoredat acceptor wavelength (680±10 nm), and “Donor”=monitored at donorwavelength (570±10 nm). These are the corrected curves (see Example 8,infra, Materials and Methods). Global fitting of the data to a 3-stepmodel gives the following rate constants: k₁=22±4 s⁻¹, k₂=4.9±0.6 s⁻¹,k₃=0.57±0.06 s⁻¹. “Acceptor+Viomycin”=in the presence of viomycinmonitored at acceptor wavelength. Here, 100 uM of viomycin waspreincubated with PRE for 1 min at 37° C. before mixing with EF-G.GTP.The small rapid decrease has a rate of 16±2 s⁻¹. The traces shown arecorrected for contributions to fluorescence change from the donor aloneand acceptor alone traces. For acceptor, the corrected trace is equal toDA−(DU+UA). For donor, the corrected trace is equal to (DA−UA)/DU. Bothtraces were globally fit to a 3-step model, A→B→C→D, in which thefluorescences of A and B are essentially equal, and the large change inFRET signal is associated with B to C conversion. The“Acceptor+Viomycin” trace measures the corrected acceptor fluorescencechange when PRE complex was pre-incubated with viomycin (100 uM) for 1min at 37° C. before mixing with EF-G.GTP.

The two rapid phases, corresponding to a lag in FRET efficiency change,followed by a large drop, proceed with apparent rate constants of 22±4s⁻¹ and 4.9±0.6 s⁻¹ (a slower third phase, k_(app) equal to 0.6±0.1 s⁻¹,occurs with a slight additional loss of FRET efficiency, reflectingslight additional tRNA movements following translocation and/or sampleheterogeneity). These values are virtually identical to those found fortranslocation using either a proflavin-labeled derivative of tRNA^(fMet)and unlabeled fMetPhe-tRNA^(Phe) or a proflavin-labeled derivative offMetPhe-tRNA^(Phe) and unlabeled tRNA^(fMet) (Pan et al., 2007),demonstrating the functionality of Cy-labeled derivatives intranslocation.

In Pan et al. (2007) evidence was presented to the effect that the firstphase of reaction corresponds to the formation of an intermediatecomplex (INT) in which the two tRNAs adopt hybrid orientations, withtRNA^(fMet) in a P/E site and tMetPhe-tRNA^(Phe) in an A/P site. It wasalso shown that viomycin allowed tRNA^(fMet) movement into a P/E hybridsite, while blocking fMetPhe-tRNA^(Phe) in the A-site. It is shownherein that added viomycin allows only a very small drop in FRETefficiency, with an apparent rate constant (16±2 s⁻¹) similar to that ofthe first phase of translocation, and that formation of INT from PREalso occurs with little change in FRET efficiency. These results implythat the distance between the core regions of the two tRNAs, to whichthe Cy dyes are attached, undergoes little change either duringmigration of tRNA^(fMet) from the P- to the P/E site, or during INTcomplex formation from PRE complex. These results are consistent withthe hypothesis that INT complex formation from PRE complex primarilyinvolves movements of the flexible 3′-single-stranded regions of thetRNAs, whereas INT to POST conversion requires the considerable distancechange between the tRNA cores that accompanies overall PRE to POSTconversion.

Poly(U) dependent poly(Phe) synthesis. Poly(Phe) synthesis bypoly(U)-programmed ribosomes was conducted in parallel with bothunlabeled Phe-tRNA^(Phe) and Phe-tRNA^(Phe)(Cy3). The results obtained(FIG. 8) shows that both tRNAs have similar activity during the initial,rapid phase of reaction, although the labeled tRNA is less active in theslower second phase of reaction. In FIG. 8, each data point is theaverage of two independent experiments.

Example 8—Materials and Methods

Enzyme and tRNA. The bacterial expression clone of yeast Dus1p with aC-terminal His tag was a gift of Dr. Eric Phiziky (U. Rochester). Thefusion protein was purified from E. coli BL21(DE3) by sonication (in 20mM Tris-HCl, pH 7.5, 50 mM NaCl, 4 mM MgCl₂, and 10% glycerol), bindingto the His-link metal affinity resin (in the sonication buffer), andelution by 200 mM imidazole. Protein concentration was determined by theBradford assay. The purified Dus1p enzyme was stored in 20 mM Tris-HCl,pH 7.5, 2 mM EDTA, 4 mM MgCl₂, 1 mM DTT, 50 mM NaCl, and 50% glycerol at−20° C. The gene for E. coli tRNA^(Pro/UGG) was cloned into the pTFMavector. Restriction of the gene with BstN1 provided a template for invitro transcription by T7 RNA polymerase (Hou, 1993). The transcript waspurified by a denaturing PAGE, visualized by UV shadowing, and extractedfrom the gel into TE (10 mM Tris-HCl, pH 8.0, 1 mM EDTA). Theconcentration of the transcript was determined by absorption at 260 nm,based on 1 OD=40 μg/mL tRNA.

Modification of tRNA Transcript by Purified Dus1p.

The tRNA transcript (in 20 μM concentrations) was heat-cooled before usein a typical Dus1p reaction containing 100 mM Tris-HCl, pH 8.0, 100 mMNH₄Ac, 5 mM MgCl₂, 2 mM dithiothreitol (DTT), 0.1 mM EDTA, 1 mM β-NADH(Sigma N1161), 1 mM NADPH (Sigma N6505), 250 μM FAD (Sigma F6625), andpurified Dus1p (˜5 μM) in a total volume of 50 μL. After incubation at30° C. for at least 40 min, the tRNA transcript was purified by phenolextraction and ethanol precipitation.

Primer Extension.

Indicated amounts of tRNA were denatured in 0.1 M KOH at 37° C. for 20min, and then neutralized with an equal volume of 5× annealing buffer(250 mM Tris-HCl, pH 8.3, 150 mM NaCl, 50 mM DTT). The tRNA (0.6 or 1.2μg) was subjected to primer extension with AMV reverse transcriptase (2units, Roche) at 42° C. for 30 min. The primer (6 pmole) was 5′ labeledwith γ-³²P-ATP by T4 polynucleotide kinase and hybridized to the tRNAsubstrate. The reaction was stopped by phenol/chloroform extraction,ethanol precipitated, and analyzed on a 12% PAGE/7M urea gel.

Rhodamine Labeling of tRNA.

Fluorescent labeling of tRNA with rhodamine was performed in the dark.Rhodamine 110 (Fluka #83695) was dissolved in 8 mg/mL in methanol,stored in the dark at −20° C. In a 20 μL reaction, the D-containing tRNAtranscript (1800 pmole in 40 mM Tris-HCl, pH 7.5) was treated with NaBH₄(100 mg/mL in 10 mM KOH) at a final concentration of 10 mg/mL for 60 minat room temperature on a shaker. The reaction was stopped by loweringthe pH to 4-5 by gradually adding 6 M acetic acid. After the tRNA wasprecipitated and washed, it was resuspended in the order of 5 μL water,85 μL of 0.1 M NaCO₂H (pH 3.0), and 10 μL rhodamine 110 (0.022 M) andincubated at 37° C. for 90 min. The reaction was then adjusted to pH 7.5by addition of 2 M Tris-HCl, pH 8.5. The tRNA was phenol extracted (pH4.3), ethanol precipitated, and resuspended in water. Absorption wasdetermined at 260 nm and 512 nm. Fluorescent labeling of tRNA withproflavin was performed in an essentially identical manner, followingWintermeyer & Zachau (1979), except that incubation at 37° C. was for 45mM.

Colorimetric Assay for Dihydrouridine.

The assay was performed as previously described (Jacobson & Hedgcoth,1970) with some modifications. The D-containing tRNA (at variousconcentrations in 100 μL of water) was hydrolyzed by adding 10 μL of 1 MKOH and incubating at 37° C. for 30 min. The reaction was thenneutralized by adding 50 μL of concentrated H₂SO₄, followed by 100 μL ofa 1:1 mixture (v:v) of 3% diacetyl monoxime (2,3-butanedione 2-oxime,Fluka #31550) and saturated N-phenyl-ρ-phenylenediamine-HCl (200 mg(Fluka #07920) in 100 mL 10% ethanol). Ureido groups were exposed byheating the reaction at 95° C. for 5 min, then at 50° C. for 5 min. Asolution of 100 μL of 1 mM FeCl₃ in concentrated H₂SO₄ was added toreact with the ureido group. After the reaction cooled to roomtemperature, absorption was read at 550 nm. A control sample withouttRNA was performed in parallel and used as a blank.

Purification of Rhodamine-Labeled tRNA.

The transcript of E. coli tRNA^(Pro/UGG) labeled with rhodamine (880pmole) was hybridized to a complementary chimeric oligonucleotide (1000pmole) 5′-mU-mG-mC-mG-mC-mU-mA-mC-CAAG-mC-mU-mG-mC-mG-3′, where “m”designates a 2′-O-methyl backbone (Hou et al., 2006). After annealing,the mixture (in 40 μL) and was digested with purified E. coli RNase H(50 μM) at 37° C. for 1 hour. The RNase H-resistant labeled transcriptwas separated from the RNase H-cleaved unlabeled transcript by 12%PAGE/7M urea on a BioRad minigel apparatus. The labeled transcript wasextracted from the gel, ethanol precipitated, and resuspended in TE.

Fluorescence Measurement of Rhodamine-Labeled tRNA.

The emission spectrum of purified rhodamine-labeled E. colitRNA^(Pro/UGG) (0.012 μM in water) was recorded from 510 to 600 nm usingan excitation wavelength of 498 nm in a model QM-4 fluorimeter (PhotonTechnology International). The rhodamine-labeled native yeast tRNA^(Phe)was run as a control.

Aminoacylation of tRNA.

Aminoacylation with proline was carried out as described (Lipman et al.,2002), using the purified D. radiodurans ProRS (Zhang & Hou, 2004) at1.0 μM for the unlabeled transcript of E. coli tRNA^(Pro/UGG) (2.0 μM)and at 10.0 μM for the rhodamine-labeled transcript (2.0 μM). Reactionswere incubated at 37° C. and aliquots were removed at various timeintervals and precipitated in 5% TCA. Aminoacylation with phenylalaninewas performed in similar conditions, but with 30 μM ¹⁴C-phenylalaine(870.3 dpm/pmol), 100 mM Tris-HCl (pH 8.0), 10 mM ATP, 50 mM Mg(OAc)₂,2.5 mM EDTA (pH 8.0), 3 mM β-mercaptoethanol, and 7 mg/mL crudesynthetase (˜100 μM) at 37° C. for 20 min.

Poly(Phe) Assay.

Ribosomes 70S (15 pmol) were programmed with 15 mg polyU, E. coli³H-AcPhe-tRNA^(Phe) in 15 μL reaction buffer (50 mM Tris-HCl (pH 7.5),70 mM NH₄Cl, 10 mM Mg(OAc)₂, 1 mM DTT) for 5 min at 37° C. Then 30 pmolEF-Tu, 30 pmol EF-G, 180 pmol yeast ¹⁴C-Phe-tRNA^(Phe), 30 nmol GTP, 25nmol phosphoenolpyruvate, 0.25 mg pyruvate kinase, 140 nmolβ-mercaptoethanol were added to make a final volume of 50 μL. Themixture was then aliquoted into 4 μL portions for each point for acidprecipitation.

Additional Labeling, Charging and Purification Procedures.

Reduction of tRNA^(fMet) and tRNA^(Phe) was performed by incubating 2.5mg/ml tRNA, 10 mg/ml NaBH₄ (dissolved in small volume of 10 mM KOH) in40 mM Tris-HCl (pH 7.5) at 0° C. for 60 min. 3 times of ethanolprecipitation was followed to remove the extra NaBH₄. To label the tRNAsthe dried pellets were dissolved in 40 μl of 0.1 M sodium formate (pH3.7), and mixed with 10 μl of 200 mM Cy3- or Cy5-hydrazide in DMSO, andincubated at 37° C. for 2 hr, followed by drying in the vacuum, 2 timesof extraction with buffer saturated phenol and 2 times of ethanolprecipitation at pH 6.0 to remove the extra dye.

tRNA^(fMet) (labeled or unlabeled) was charged and formylated byincubating 20 μM tRNA^(fMet), 80 μM [³⁵S]-methionine, 720 μM folinicacid (as a formyl donor), and 1/10 volume of crude E. coliaminoacyl-tRNA synthetases (containing formyl transferase) in 100 mMTris-HCl (pH 7.8), 4 mM ATP, 20 mM MgCl₂, 1 mM EDTA, 10 mM KCl, and 7 mM2-mercaptoethanol at 37° C. for 20 min. Yeast tRNA^(Phe) (labeled,unlabeled, or NaBH₄ treated) was charged by incubating 20 μM tRNA^(Phe),80 μM [³H]-phenylalanine, 1/10 volume of partially purified yeastsynthetase in 100 mM Tris-HCl (pH 8.0), 10 mM ATP, 50 mM MgAc₂, 2.5 mMEDTA, 3 mM 2-mercaptoethanol at 37° C. for 20 min. For tRNA^(fMet) Cy5labeling was performed before charging. For tRNA^(Phe) because of thelow charging efficiency of Cy3-tRNA^(Phe) a modified protocol was usedfor later experiments, in which the NaBH₄-treated tRNA^(Phe) was chargedfirst, followed by HPLC separation of charged from uncharged tRNA^(Phe)(see below), and then labeled. tRNA^(Lys) was charged with pureHis-tagged E. coli Lys-RS, purified on a Ni-NTA (Qiagen) column, byincubating 20 μM tRNA^(Lys), 80 [¹⁴C]lysine, and 1 μM Lys-RS in 100 mMTris-HCl (pH 7.8), 4 mM ATP, 20 mM MgCl₂, 1 mM EDTA, and 7 mM2-mercaptoethanol at 37° C. for 10 min. Purification of the charge tRNAswere carried out on FPLC using a MonoQ column with a gradient of 0-1 MNaCl in 50 mM Na acetate (pH 5.0).

HPLC purification of Phe-tRNA^(Phe) was conducted on a phenylreverse-phase column (4.6×250 mm), with a gradient of 0-24% methanol in20 mM NH₄Ac (pH 5.5) and 50 mM NaCl. Phe-tRNA^(Phe) formed after NaBH₄treatment had essentially the same profile has the untreatedPhe-tRNA^(Phe). To purify labeled tRNA^(fMet) or tRNA^(Phe) fromunlabeled tRNA a Mono-Q anion-exchange column was used on FPLC with agradient of 0.5-0.9 M NaCl in 50 mM NaAc (pH 6.0). The final product ofCy5-fMet-tRNA^(fMet) was 0.70-0.75 Cy5/tRNA^(fMet), and 590 pmol/A260,and Cy3-Phe-tRNA^(Phe) was 1.0 Cy3/tRNA^(Phe), and 1190 pmol/A260.

Sample Preparation.

Tight-coupled ribosomes from E. coli MRE600 cells, mRNA022, unlabeledfMet-tRNA^(fMet) and Phe-tRNA^(Phe), and cloned E. coli His-taggedproteins EF-G, EF-Tu, IF1, IF2, and IF3 were prepared as described (Panet al., 2008). mRNA-MFK was ordered from Dharmacon with the followingsequence: GGG AAG GAG GUA AAA AUG UUU AAA CGU AAA UCU ACU. E. colitRNA^(fMet), tRNA^(Lys), and yeast tRNA^(Phe) were obtained fromChemical Block.

30Sic Formation.

The concentrations given are final. For IF2-Cy3 fluorescence change 0.45μM each of fMet-tRNA^(fMet), IF1, and IF3, 0.90 μM mRNA022, 100 μM GTP,and 0.30 μM 30S were preincubated at 37° C. for 15 min, and then rapidlymixed with 0.15 μM Cy3-IF2 in buffer A at 20° C. on a stopped flowapparatus, excited at 530 nm and monitored through a bandpass 550±10 nmfilter. For Cy5-fMet-tRNA^(fMet) change 0.45 μM each of IF1, IF2, andIF3, 0.90 μM mRNA022, 100 μM GTP, and 0.30 μM 30S were incubated at 37°C. for 15 min, before rapidly mixed with 0.15 μM Cy5-fMet-tRNA^(fMet) inbuffer A at 20° C., excited at 650 nm and monitored via a bandpass680±10 nm filter.

Complex Formation.

70SIC was formed by incubating 2 μM 70S ribosome, 8 μM mRNA-MFK, 3 μMeach of IF1, IF2, IF3, and fMet-tRNA^(fMet), and 1 mM GTP in Buffer A(50 mM Tris-HCl (pH 7.5), 70 mM NH₄Cl, 30 mM KCl, 7 mM MgCl₂, 1 mM DTT)for 25 min at 37. TC was formed by incubating 6 EF-Tu, 3 μMPhe-tRNA^(Phe), 1 mM GTP, 1.5 mM phosphoenolpyruvate, and 0.5 mg/Lpyruvate kinase in buffer A for 5 min at 37° C. PRE complex was formedby incubating 1 μM 70SIC with 1.5 μM TC for 0.5 min at 37° C., andpurified by centrifugation through a 1.1 M sucrose cushion (450,000 g,40 min, 4° C.) in Buffer B (same as buffer A but with 20 mM MgCl₂). Thepellet was resuspended in buffer C (20 mM HEPES-KOH (pH 7.6 at 0° C.),4.5 mM MgAc₂, 4 mM 2-mercaptoethanol, 150 mM NH₄Ac, 0.05 mM spermine,and 2 mM spermidine) to a concentration of about 5 μM, and stored in a−80° C. freezer before being used.

Fret Measurements.

The steady state fluorescence spectra of 0.1 μM PRE, POST (PRE+0.5 μMEF-G+1 mM GTP), and POST2 (PRE+0.5 μM EF-G, 1 mM GTP, 0.3 μM[¹⁴C]-Lys-tRNA^(Lys) and 0.5 μM EF-Tu) complexes in buffer C weremeasured on a Fluorolog-3 spectrofluorometer (Horiba Jobin Yvon) with anexcitation wavelength of 518 nm. Each trace is an average of 3 traces.Experiments with both donor Cy3-Phe-tRNA^(Phe), and acceptorCy5-fMet-tRNA^(fMet) (DA) were run in parallel with donor alone (DU) oracceptor alone (UA).

For rapid kinetics FRET, PRE complex was rapidly mixed with 2 μMEF-G.GTP in buffer A at 25° C. on a SX.18MV stopped-flowspectrofluorometer (Applied Photophysics). Buffer A is used here tocompare with previous results (Pan, 2007). The excitation wavelength was518 nm. Donor was monitored using 570±10 nm bandpass filter and theacceptor was monitored using 680±10 nm bandpass filter. Correction wasmade by FRET=DA−DU−UA for acceptor change, and FRET=(DA−UA)/DU for donorchange. A lag and two exponential phases are seen in both the donorincrease and acceptor decrease traces. These two traces are fit globallyby Scientist using A→B→C→D, where fluorescence values of A and B are setto be identical. The acceptor trace in the presence of viomycin (100 μM)is fit by a single-exponential term plus a slope term.

Poly(Phe) Assay.

Assay was carried out in buffer D (20 mM Tris-HCl (pH 7.6), 200 mMNH₄Cl, 10 mM MgAc₂), and the concentrations given below are finalconcentrations. Initiation complex was formed by mixing poly(U) 0.3μg/ul, 0.3 μM 70S ribosome, and 0.36 μM [³H]-AcPhe-tRNA^(Phe) at 37° C.for 5 min, and then mixed with 2.8 μM 2-mercaptoethanol, 0.005 mg/mlpyruvate kinase, 0.6 μM GTP, 4 μM [³H]-Phe-tRNA^(Phe) (Cy3 labeled orunlabeled), 0.6 μM EF-G in a volume of 50 μl. 0.6 μM EF-Tu was added toinitiate the reaction at 37° C., and aliquots were taken at time pointsand added to 0.3 ml 5% TCA, heated to 95° C. for 15 min, cooled on iceand filtered through a nitrocellulose filter with 5×1 ml washes with 5%cold TCA. A point was taken before addition of EF-Tu as the background.

Distance Calculation.

Equation (1) is used to calculate distance between the two fluorophores.R₀ is the Förster distance of this pair of donor and acceptor at whichthe FRET efficiency is 50%. R₀ of Cy3 and Cy5 is assumed to be 50 {acuteover (Å)}. E is the FRET efficiency calculated by relative donordecrease (last column in Table 2, supra) and a correction factor of 0.75(labeling efficiency of Cy5-tRNA^(fMet)).

$\begin{matrix}{r = {R_{0}\left( {\frac{1}{E} - 1} \right)}^{1/6}} & (1)\end{matrix}$

REFERENCES CITED

-   Betteridge T, Liu H, Gamper H, Kirillov S, Cooperman B S, Hou Y M.    Fluorescent labeling of tRNAs for dynamics experiments. RNA. 2007    September; 13(9):1594-601.-   Bieling P, Beringer M, Adio S, Rodnina M V. Peptide bond formation    does not involve acid-base catalysis by ribosomal residues. Nat    Struct Mol Biol. 2006 May; 13(5):423-8.-   Bishop A C, Xu J, Johnson R C, Schimmel P, de Crecy-Lagard V. 2002.    Identification of the tRNA-dihydrouridine synthase family. J Biol    Chem 277:25090-25095.-   Blanchard S C, Kim H D, Gonzalez R L, Jr., Puglisi J D, Chu S.    2004a. tRNA dynamics on the ribosome during translation. Proc Natl    Acad Sci USA 101:12893-12898.-   Blanchard S C, Gonzalez R L, Kim H D, Chu S, Puglisi J D. 2004b.    tRNA selection and kinetic proofreading in translation. Nat Struct    Mol Biol 11:1008-1014.-   Boonacker E, Van Noorden C. 2001. Enzyme cytochemical techniques for    metabolic mapping in living cells with special reference to    proteolysis. J Histochem Cytochem 49:1473-1486.-   Cerutti P, Miller N. 1967. Selective reduction of yeast transfer    ribonucleic acid with sodium borohydride. J Mol Biol 26:55-66.-   Cochella L, Green R. 2005. An active role for tRNA in decoding    beyond codon:anticodon pairing. Science 308:1178-1180.-   Grigoriadou C, Marzi S, Kirillov S, Gualerzi C O, Cooperman B S. A    quantitative kinetic scheme for 70 S translation initiation complex    formation. J Mol Biol. 2007a Oct. 26; 373(3): 562-72-   Grigoriadou C, Marzi S, Pan D, Gualerzi C O, Cooperman B S. The    Translational Fidelity Function of IF3 During Transition from the 30    S Initiation Complex to the 70 S Initiation Complex. J Mol Biol.    2007b Oct. 26; 373(3):551-61.-   Hirsh D. 1971. Tryptophan transfer RNA as the UGA suppressor. J Mol    Biol 58:439-458.-   Horobin R W, Stockert J C, Rashid-Doubell F. 2006. Fluorescent    cationic probes for nuclei of living cells: why are they selective?    A quantitative structure-activity relations analysis. Histochem Cell    Biol 126:165-175.-   Hou Y M. 1993. The tertiary structure of tRNA and the development of    the genetic code. Trends Biochem Sci 18:362-364.-   Hou Y M, Li Z, Gamper H. 2006. Isolation of a site-specifically    modified RNA from an unmodified transcript. Nucleic Acids Res    34:e21.-   Jacobson M, Hedgcoth C. 1970. Determination of 5,6-dihydrouridine in    ribonucleic acid. Anal Biochem 34:459-469.-   Jencks, W. P. Mechanism and catalysis of simple carbonyl group    reactions. Prog. Phys. Org. Chem. 1964, 2, 63-128.-   Korostelev A, Trakhanov S, Laurberg M, Noller H F. 2006. Crystal    structure of a 70S ribosome-tRNA complex reveals functional    interactions and rearrangements. Cell 126:1065-1077.-   Lipman R S, Wang J, Sowers K R, Holt Y M. 2002. Prevention of    mis-aminoacylation of a dual-specificity aminoacyl-tRNA synthetase.    J Mol Biol 315:943-949.-   Lee L G, Spurgeon S L, Heiner C R, Benson S C, Rosenblum B B,    Menchen S M, Graham R J, Constantinescu A, Upadhya K G, Cassel J M.,    New energy transfer dyes for DNA sequencing, 1997, Nucleic Acids    Res. 1997 25:2816-22.-   Levrand B, Fieber W, Lehn J-M, and Herrmann A. Controlled Release of    Volatile Aldehydes and Ketones from Dynamic Mixtures Generated by    Reversible Hydrazone Formation Helv Chim Acta 2007 90: 2281-2314-   Liu H, Musier-Forsyth K. 1994. Escherichia coli proline tRNA    synthetase is sensitive to changes in the core region of tRNA(Pro).    Biochemistry 33:12708-12714.-   McIntosh B, Ramachandiran V, Kramer G, Hardesty B. Initiation of    protein synthesis with fluorophore-Met-tRNA(f) and the involvement    of IF-2. Biochimie. 2000 82:167-74.-   Munro J B, Altman R B, O'Connor N, Blanchard S C. Identification of    two distinct hybrid state intermediates on the ribosome. Mol Cell.    2007; 25:505-17.-   Negrutskii B S, Deutscher M P. 1991. Channeling of aminoacyl-tRNA    for protein synthesis in vivo. Proc Natl Acad Sci USA 88:4991-4995.-   Pan D, Kirillov S, Cooperman B. 2007. Kinetically competent    intermediate(s) in the translocation step of protein synthesis. Mol    Cell, in press.-   Pan D, Kirillov S, Zhang C M, Hou Y M, Cooperman B S. 2006. Rapid    ribosomal translocation depends on the conserved 18-55 base pair in    P-site transfer RNA. Nat Struct Mol Biol 13:354-359.-   Pan D, Zhang C M, Kirillov S, Hou Y M, Cooperman B S. Perturbation    of the tRNA tertiary core differentially affects specific steps of    the elongation cycle. J Biol Chem. 2008 Apr. 30. [Epub ahead of    print] PMID: 18448426.-   Pape, T., Wintermeyer, W., and Rodnina, M. V., Complete kinetic    mechanism of elongation factor Tu-dependent binding of    aminoacyl-tRNA to the A site of the E. coli ribosome, 1998, Embo J.    17:7490-7497.-   Qin, H., Grigoriadou, C., and Cooperman, B. S. (manuscript in    preparation).-   Sako Y, Usuki F, Suga H, A novel therapeutic approach for genetic    diseases by introduction of suppressor tRNA Nucleic Acids. 2006.    Symp. Ser., 50, 239-240.-   Sampson J R, DiRenzo A B, Behlen L S, Uhlenbeck O C. 1989.    Nucleotides in yeast tRNAPhe required for the specific recognition    by its cognate synthetase. Science 243:1363-1366.-   Savelsbergh A, Katunin V I, Mohr D, Peske F, Rodnina M V,    Wintermeyer W. 2003. An elongation factor G-induced ribosome    rearrangement precedes tRNA-mRNA translocation. Mol Cell    11:1517-1523.-   Scala-Valero C Doizi D Guillaumet G, Synthesis of Isomers of    Rhodamine 575 and Rhodamine 6G as New Laser Dyes, 1999, Tet Lett 40    4803-4806.-   Selmer M, Dunham C M, Murphy F Vt, Weixlbaumer A, Petry S, Kelley A    C, Weir J R, Ramakrishnan V. 2006. Structure of the 70S ribosome    complexed with mRNA and tRNA. Science 313:1935-1942.-   Snustad D. P and Simmons M J 2003 Principles of Genetics John Wiley    & Sons, Hoboken, N.J.-   Sprinzl M, Horn C, Brown M, Ioudovitch A, Steinberg S. 1998.    Compilation of tRNA sequences and sequences of tRNA genes. Nucleic    Acids Res 26:148-153.-   Thiebe R, Zachau H G. A specific modification next to the anticodon    of phenylalanine transfer ribonucleic acid. Eur J Biochem. 1968    5:546-55.-   Westhof E. 2006. The ribosomal decoding site and antibiotics.    Biochimie 88:931-933.-   Wintermeyer W, Zachau H G. Replacement of Y base, dihydrouracil, and    7-methylguanine in tRNA by artificial odd bases. FEBS Lett. 1971    18:214-218.-   Wintermeyer W, Zachau H G. 1974. Replacement of odd bases in tRNA by    fluorescent dyes. Methods Enzymol 29:667-673.-   Wintermeyer W, Zachau H G. 1979. Fluorescent derivatives of yeast    tRNAPhe. Eur J Biochem 98:465-475.-   Woolhead C A, McCormick P J, Johnson A E: Nascent membrane and    secretory proteins differ in FRET-detected folding far inside the    ribosome and in their exposure to ribosomal proteins. Cell 2004,    116:725-736.-   Xing F, Hiley S L, Hughes T R, Phizicky E M. 2004. The specificities    of four yeast dihydrouridine synthases for cytoplasmic tRNAs. J Biol    Chem 279:17850-17860.-   Yusupov et al., Crystal Structure of the Ribosome at 5.5 Å    Resolution, 2001, Science 5518(292), 883-896.-   Zhang C-M, Hou Y-M. 2004. Synthesis of cysteinyl-tRNACys by a    prolyl-tRNA synthetase. RNA Biology 1:35-41.

What is claimed:
 1. A method for labeling a transfer RNA moleculecomprising: providing a substitution comprising a fluorophore bearing ahydrazide functional group at the dihydrouracil component of adihydrouridine of said transfer RNA.
 2. The method according to claim 1,wherein the transfer RNA has at least one uridine in its D loop, andfurther comprising converting said uridine to dihydrouridine prior tosubstituting at said uridine component with said fluorophore.
 3. Themethod according to claim 1 further comprising loading onto the 3′ endof said transfer RNA an amino acid corresponding to a triplet nucleotidesequence that base-pairs to the anticodon sequence of said transfer RNA.4. The method according to claim 1 further comprising subjecting saidtransfer RNA to conditions effective to load onto the 3′ end of saidtransfer RNA an amino acid corresponding to a triplet nucleotidesequence that base-pairs to the anticodon sequence of said transfer RNA.5. The method of claim 1 wherein dihydrouridine is subjected to reducingconditions.
 6. The method of claim 5 wherein the reducing conditionscomprise reacting with borohydride.
 7. A nucleic acid compositioncomprising a transfer RNA molecule including a fluorophore substitutionat the dihydrouracil component of a dihydrouridine in a D loop of thetransfer RNA, the fluorophore bearing a hydrazide functional group. 8.The composition of claim 7 wherein the fluorophore substitution is atthe dihydrouracil component of a dihydrouridine that is at a positionU16, U17, U20, or U20b on said transfer RNA.
 9. A method of assessingprotein synthesis in a translation system comprising: providing a tRNAhaving a fluorophore substitution at the dihydrouracil component of adihydrouridine in a D loop of the tRNA, the fluorophore bearing ahydrazide functional group; introducing the labeled tRNA into thetranslation system; irradiating the translation system withelectromagnetic radiation, thereby generating a fluorescence signal fromsaid fluorophore; detecting said fluorescence signal; and, correlatingsaid fluorescence signal to one or more characteristics of said proteinsynthesis in said translation system.
 10. The method according to claim9 wherein said fluorophore is a hydrazide comprising Cy3 hydrazide,Cy3.5 hydrazide, Cy5 hydrazide, Cy5.5 hydrazide, Alexa Fluor 488hydrazide, Alexa Fluor 555 hydrazide, Alexa Fluor 568 hydrazide, AlexaFluor 594 hydrazide, and Alexa Fluor 647 hydrazide, Texas Red hydrazide,Lucifer yellow hydrazide, C5-DMB-ceramide, C6 phosphatidylinositol5-phosphate, Cascade Blue hydrazide, or ATTO dye.
 11. The methodaccording to claim 9 wherein the translation system comprises acell-free system.
 12. The method according to claim 9 wherein thetranslation system comprises a living cell.
 13. The method according toclaim 9 further comprising providing at least one additionalfluorescently labeled translation component.
 14. The method according toclaim 13 wherein said fluorescently labeled translation componentcomprises a ribosome, a ribosomal protein, an initiation factor, anelongation factor, a messenger RNA, or a ribosomal RNA.
 15. The methodaccording to claim 13 wherein the fluorophore of said labeled tRNA andthe fluorophore of said at least one additional fluorescently labeledcomponent comprise a FRET pair, and wherein said detecting saidfluorescence signal comprises detecting energy transfer between thefluorophore of said labeled tRNA and the fluorophore of said at leastone additional fluorescently labeled component.
 16. The method accordingto claim 1 wherein said fluorophore is a hydrazide comprising Cy3hydrazide, Cy3.5 hydrazide, Cy5 hydrazide, Cy5.5 hydrazide, Alexa Fluor488 hydrazide, Alexa Fluor 555 hydrazide, Alexa Fluor 568 hydrazide,Alexa Fluor 594 hydrazide, and Alexa Fluor 647 hydrazide, Texas Redhydrazide, Lucifer yellow hydrazide, C5-DMB-ceramide,C6-phosphatidylinositol 5-phosphate, Cascade Blue hydrazide, or ATTOdye.